Before we begin, let me start with the trailer for the DVD release, uploaded by Batmanskiv1 to YouTube:
Factoring in commercials, this aired as a 90 minute special on Kids' WB!, a sort of expanded edition of The New Batman-Superman Adventures (so titled because the first series to use that title was Time-Warner's made-for-cable compilation of Filmation shorts and selected Super Friends cartoons that aired on USA and later Cartoon Network).
The plot is rather simple. After stealing a 20 pound dragon statue made of kryptonite, the Joker (Mark Hamill) decides to go after Superman rather than tangle again with the Batman. He has Harley Quinn (Arleen Sorkin, Days of Our Lives) carjack the personal limo of Metropolis' most prominent businessman (and a corrupt one at that), Lex Luthor (Clancy Brown), and forges a deal with Luthor to eliminate the Man of Steel once and for all.
Coincidentally, of course, Bruce Wayne (Kevin Conroy) is in Metropolis on business, as he's entered into a deal with Luthor to build weapons, which Luthor wants to use for domestic defense. Reporter Lois Lane (Dana Delany, ex-China Beach) is smitten with Wayne, and finds the affection is mutual, at least for now. That doesn't sit well with Superman (Tim Daly, ex-Wings), who's not too fond of the Dark Knight visiting his town, either.
As for the villains of the piece, all is not well, either. Quinn can't get along with Luthor's personal chauffeur/bodyguard, Mercy Graves (Lisa Edelstein, now on House), and Luthor's deal with the Joker is tenuous at best (what a shock). If you follow the comics, you have a pretty good idea on how this is all going to end.